import sys
import os
species_name_list=['Tomato','Potato','viarum','lyratum','melongena','Pepper','biflora','Golden','Datura','Wolfberry']
index_name_list=['1','2','3','4','5','6','10','7','9','8']

for i,j in zip(species_name_list,index_name_list):
    # if i!='Wolfberry':
    #     continue
    # command1='python get_lost_gene_TE_density3.py '+i+'.syn_bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge '+i+'.syn_TE &'
    # command1='python get_lost_gene_TE_density2.py '+i+'.loss_body.bed '+i+'loss_flank.bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge '+i+'loss_TE &'
    # command1='python get_lost_gene_TE_density3.py '+i+'.loss_bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge '+i+'.loss_TE &'
    # command1='python get_lost_gene_TE_density3.py '+i+'.trans_bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge '+i+'.trans_TE &'
    
    ###最近用的命令 脚本里可以自己提取上下游
    command1='python get_lost_gene_TE_density4.py '+i+'.trans_bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge ../../sola_10_species_hight_1119/mSynF'+j+'/species.gff_pos '+i+'.trans_TE &'
    command2='python get_lost_gene_TE_density4.py '+i+'.syn_bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge ../../sola_10_species_hight_1119/mSynF'+j+'/species.gff_pos '+i+'.syn_TE &'
    command3='python get_lost_gene_TE_density4.py '+i+'loss_body.bed ../annot/'+i+'.mod.EDTA.TEanno.gff3.merge ../../sola_10_species_hight_1119/mSynF'+j+'/species.gff_pos '+i+'.loss_TE &'
    print(command1)
    os.system(command1)
    os.system(command2)
    os.system(command3)